sushi_fabric 1.1.2 → 1.1.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 3749f2baffa9e17e37e26e36d5942bcef0d70d0ad6e1b34844892e48ab2e9482
+  metadata.gz: 9fedc477c136f74445e146138c9e0aa66be6fb2ab0c01da53c88827f19ac6363
+  data.tar.gz: 935cee957707889446cbd842e506551cb6269a38f71ad300e3c828bdac6790a0
 SHA512:
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+  metadata.gz: 42da71dbf0da6dab834e42f943d2dd0fb8a8a29598e8274927abb2233fc9db15953961adb60fd99ce45ed265ea7d33e3f77949be7c6aaf05c9699d7c69ba94d0
+  data.tar.gz: 79f887cb36630cbc1ad3c8d8b1b8c6431348a5707cc83db17572223724ea275e6564c2ca885cbe52b7d427fb1ddafa69cd50db96d101797b266852b088861345

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20211015-142855'
+# Version = '20220127-101054'
 
 require 'csv'
 require 'fileutils'
@@ -240,8 +240,6 @@ class SushiApp
     @params['cores'] = nil
     @params['ram'] = nil
     @params['scratch'] = nil
-    @params['node'] = ''
-    @params['queue'] = ''
     @params['partition'] = ''
     @params['process_mode'] = 'SAMPLE'
     @params['samples'] = ''
@@ -386,14 +384,23 @@ class SushiApp
     @result_dir = File.join(@project, @result_dir_base)
     @scratch_result_dir = File.join(SCRATCH_DIR, @result_dir_base)
     @job_script_dir = File.join(@scratch_result_dir, 'scripts')
+    @uploaded_files_dir = File.join(@scratch_result_dir, 'uploaded')
     @gstore_result_dir = File.join(@gstore_dir, @result_dir)
     @gstore_script_dir = File.join(@gstore_result_dir, 'scripts')
     @gstore_project_dir = File.join(@gstore_dir, @project)
+    @gstore_uploaded_dir = File.join(@gstore_result_dir, 'uploaded')
     set_file_paths
   end
   def prepare_result_dir
     FileUtils.mkdir_p(@scratch_result_dir)
     FileUtils.mkdir_p(@job_script_dir)
+    @uploaded_files = []
+    @params.each do |key, value|
+      if @params[key, 'file_upload']
+        FileUtils.mkdir_p(@uploaded_files_dir)
+        @uploaded_files << value
+      end
+    end
   end
   def check_latest_modules_version(modules)
     command_out =  %x[ bash -lc "source #{@module_source}; module whatis #{modules.join(" ")} 2>&1" | cut -f 1 -d " " | uniq ]
@@ -517,6 +524,7 @@ rm -rf #{@scratch_dir} || exit 1
     gsub_options << "-p #{@params['partition']}" unless @params['partition'].to_s.empty?
     gsub_options << "-r #{@params['ram']}" unless @params['ram'].to_s.empty?
     gsub_options << "-s #{@params['scratch']}" unless @params['scratch'].to_s.empty?
+    gsub_options << "-i #{@params['nice']}" unless @params['nice'].to_s.empty?
     command = "wfm_monitoring --server #{WORKFLOW_MANAGER} --user #{@user} --project #{@project.gsub(/p/,'')} --logdir #{@gstore_script_dir} #{job_script} #{gsub_options.join(' ')}"
     puts "submit: #{command}"
 
@@ -578,7 +586,14 @@ rm -rf #{@scratch_dir} || exit 1
     CSV.open(file_path, 'w', :col_sep=>"\t") do |out|
       out << ["sushi_app", self.class.name]
       @output_params.each do |key, value|
-        out << [key, value]
+        if @output_params[key, 'file_upload']
+          uploaded_file_path = File.join(@result_dir, "uploaded", File.basename(value))
+          out << [key, uploaded_file_path]
+          @params[key] = uploaded_file_path
+          @output_params[key] = uploaded_file_path
+        else
+          out << [key, value]
+        end
       end
     end
     file_path
@@ -630,6 +645,18 @@ rm -rf #{@scratch_dir} || exit 1
     end
     com
   end
+  def copy_uploaded_files
+    if not @uploaded_files.empty?
+      @uploaded_files.each do |file|
+        FileUtils.cp(file, @uploaded_files_dir)
+        command = "cp #{file} #{@uploaded_files_dir}"
+        puts command
+        FileUtils.rm_r(File.dirname(file))
+        command = "rm -rf #{File.dirname(file)}"
+        puts command
+      end
+    end
+  end
   def copy_inputdataset_parameter_jobscripts
     org = @scratch_result_dir
     dest = @gstore_project_dir
@@ -780,6 +807,12 @@ rm -rf #{@scratch_dir} || exit 1
       data_set.id
     end
   end
+  def save_parameters_in_sushi_db
+    if @next_dataset_id and next_dataset = DataSet.find_by_id(@next_dataset_id)
+      next_dataset.job_parameters = @output_params
+      next_dataset.save
+    end
+  end
   def main(mock=false)
     ## sushi writes creates the job scripts and builds the result data set that is to be generated
     @result_dataset = []
@@ -826,6 +859,7 @@ rm -rf #{@scratch_dir} || exit 1
       unless NO_ROR
         @current_user ||= nil
         @next_dataset_id = save_data_set(data_set_arr.to_a.flatten, headers, rows, @current_user, @child)
+        save_parameters_in_sushi_db
 
         unless @off_bfabric_registration
           if next_dataset = DataSet.find_by_id(@next_dataset_id)
@@ -842,6 +876,7 @@ rm -rf #{@scratch_dir} || exit 1
         end
       end
     end
+    copy_uploaded_files
     copy_inputdataset_parameter_jobscripts
 
     # job submittion

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "1.1.2"
+  VERSION = "1.1.6"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.1.2
+  version: 1.1.6
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-10-15 00:00:00.000000000 Z
+date: 2022-01-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler